Table 2.

A table highlighting open source software compatible with imaging mass spectrometry datasets, note vendor proprietary software is not included as this is instrument dependent, whereas many of these open source platforms are compatible with many different types of datasets.

Name	Function	Website	Documentation	Availability	Ref.
Cardinal	R package for imaging mass spectrometry preprocessing, statistical analysis, and visualization	https://bioconductor.org/packages/release/bioc/html/Cardinal.html	https://bioconductor.org/packages/release/bioc/vignettes/Cardinal/inst/doc/Cardinal-2-guide.html	Offline	57
MSiReader v1.0	MATLAB/standalone tool for imaging mass spectrometry quantification, quality assessment, and visualization	https://msireader.wordpress.ncsu.edu/	http://bitly.com/MSiReaderUsersManual	Offline	58
microMS	Python based tool for single-cell microscopy-based imaging mass spectrometry data analysis	http://neuroproteomics.scs.illinois.edu/microMS.htm	http://neuroproteomics.scs.illinois.edu/Site/microms/microMS_UserGuide.pdf	Offline	59
msIQuant	C++ based tool for imaging mass spectrometry preprocessing, quantitation, and visualization	https://ms-imaging.org/wp/paquan/	Included in installation files	Offline	60
OmniSpect	MATLAB based tool/web server for imaging mass spectrometry visualization and statistical analysis	http://cs.appstate.edu/omnispect/ (web server) https://github.com/rmparry7/omnispect/ (standalone)	https://github.com/rmparry7/omnispect/blob/master/README.txt (standalone)	Online/ Offline	61
CycloBranch	Cross platform tool for dereplication and de novo sequencing of nonribosomal peptides and polyketides	https://github.com/rmparry7/omnispect/blob/master/README.txt	https://ms.biomed.cas.cz/cyclobranch/docs/html/userguide.html	Offline	62